RunCoNGA | R Documentation |
Runs CoNGA on a seurat object
RunCoNGA(
seuratObj = NULL,
tcrClonesFile = NULL,
seuratToCongaDir = "./seuratToConga",
assayName = "RNA",
organism = NULL,
runCongaOutputFilePrefix = "conga_output",
gexDatatype = "10x_h5",
runCongaOutfilePrefixForQcPlots = "qc_plots",
runCongaOutputDirectory = "./conga_output",
congaMetadataPrefix = "conga_",
pngConversionTool = NULL
)
seuratObj |
The Seurat object containing the data to be run using CoNGA. |
tcrClonesFile |
The 10x clonotypes file for this Seurat object. Single lanes can use the CellRanger/Vloupe contigs CSV file. Merged lanes need to merge these files and modify them to create unique cellbarcodes and clonotype names, such as the code from Rdiscvr::CreateMergedTcrClonotypeFile(). |
seuratToCongaDir |
The directory to store the results of SeuratToCoNGA() (the input files for the python call to run_CoNGA()). |
assayName |
Pass-through variable for accessing the assay name within the Seurat object for SeuratToCoNGA(). |
organism |
'human' or 'rhesus' |
runCongaOutputFilePrefix |
prefix for the output files from the python call to run_CoNGA(). |
gexDatatype |
This should be "10x_h5" since we're using DropletUtils to write the counts, although "h5ad" is supported. |
runCongaOutfilePrefixForQcPlots |
Prefix for the qc output files to be generated by run_CoNGA(). |
runCongaOutputDirectory |
The directory that will store the many files created during run_CoNGA(). |
congaMetadataPrefix |
A prefix to be added to the columns of the metadata that will be added from CoNGA within the returned Seurat object. |
pngConversionTool |
specify the conversion tool used by CoNGA for svg to png conversion. Can be any of: convert, inkscape, rsvg |
A Seurat object with the conga metadata relevant to TCR + gene expression clustering appended.
## Not run:
CreateMergedTcrClonotypeFile(seuratObj,
outputFile = "./tcrs.csv")
congaSeuratObj <- RunCoNGA(seuratObj = seuratObj,
tcrClonesFile = "./tcrs.csv",
organism = "rhesus")
## End(Not run)
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